The Vaxi Atrocity is an event from the Dark Heresy Second Edition splatbook Enemies Within.
The Vaxi atrocity started when a bunch of Ordo Hereticus Inquisitors decided to hold a conclave around 729.M41. The veteran Witch Hunter Lord Spiron Hark and his followers wanted to investigate, and, if need be, purge the Askellian nobility to get at the hidden secrets of the sector. Seeing as the sector was notoriously corrupt and that its ruling classes were deeply involved, it seemed to be a plan all Inquisitors could agree on. However, Lord Hark was a notorious bombast and a Puritan through and through, and as such had garnered more than his fair share of rivals and enemies within the ranks of the Inquisition over the decades of his service. They opposed his plans, apparently simply to frustrate Hark’s rise in power and influence rather than because they objected to the course of action itself. After he demanded immediate and extreme action, a fierce argument erupted in the hallowed vaults of the Oblitia Cathedra where the conclave was held on the edge of the Sector, soon followed by insults and accusations so severe they could not be withdrawn without substantial loss of face. Centuries of accumulated ill-will, anger, and virulent mistrust amongst the Inquisitors operating in Askellon seemed to quickly boil over to impossible levels. Hark initially gathered his household and his allied peers to leave the conclave for the inner Askellian worlds: he declared to the assembled Inquisitors that he would have the truth, one way or the other, and with or without the blessings of those opposed to his direction.
Inquisitor Hark’s opponents, despite appearances, were not complete idiots or heretics. Rather, it was because two decades before, they had instigated their own infiltration of the sector for their own ends, and feared that Hark’s interference would ruin their work. Exactly what that work amounted to or was aimed towards appears to be a secret these Radicals took to their graves. Enemies Beyond states that there was another plot in progress, this one having begun several centuries earlier: Inquisitorial agents had been attempting to integrate the higher spheres of Askellon nobility discreetly to search for proof of a deep-seated corruption, and after generations of careful plotting some agents were about to marry into some of these Houses when the Vaxi Atrocity disrupted the entire sector and ruined their plans. Things get confusing here, because it seems to be implied that this is the plan the Radicals had, yet the last two sentences should make it obvious that the timeframes just don't match up between what's stated in both books. Continuity error or simple increase in the complexity of the plotting overdose?
Upon the disbandment of the assembly, both factions set out for the sector’s core, sweeping up what allies they could along the way and utilizing their powers as Inquisitors to requisition what assets they encountered. As the rival groups penetrated deeper into the Rubicon Sub-Sector, they called upon ever-greater forces, and entire regiments of the Imperial Guard mustered at their order from a swathe of worlds along a route many parsecs in length. By the time they crashed headlong into Rubicon, all pretense at due process was shed. Entire worlds were burning before the Lords of Askellon had any notion what was occurring, because they were incompetent and traitorous fucktards who probably deserved death anyway. Sector-wide defence protocols were set in motion, but while the defenders had experience fighting uprisings, prosecuting mutant culls, and even stalling xenos invasions, none could face the might of the Inquisition and of the yet-faithful armies of the Imperium.
At length, the Sector Praefect, at that time Lord Vhinjet Romonav VII, declared war upon the invaders. His declaration was a strident statement, which began as a warning, but soon meandered into what amounted to an admission of heresy. Entire generations of savants have debated whether Romonav intended to broadcast the message he did, or if he was overcome by hubris, misunderstood, caught in the grips of insanity, or even possessed by some daemonic entity. Regardless of the truth, by the end of the message, which was transmitted using every Astropathic choir on Juno and spread across Askellian space, the Praefect had, with deliberate intent or otherwise, announced his sector’s secession from the Imperium of Man. This man's wife was apparently either an Inquisitorial Agent who manipulated him into doing this to preserve the Inquisition in the sector by stopping them from all killing each other, or a servant of Chaos that replaced her. The Praefect may have been a heretic that revealed himself in the worst way at the worst time (for him), or he may actually have been an innocent manipulated by the Inquisition (or possibly Chaos) to either protect the Inquisition as a whole in the sector, or advance/protect another grand plan. No-one really knows, and the people who did know either died mysteriously or didn't manage to transmit the necessary information before they died. And you thought the Calixis Sector was too full of plots!
Confronted with treachery on such a massive scale and mindful of those shreds of the sector’s history they had access to, the opposing Inquisitorial factions ceased their internecine battle. Immediately, they fell upon Vaxi and the millions of Askellian troops mustered there with power and potency surely not seen since the Macharian Crusade. The combined forces massacred the defenders in a crusade so bloody none were spared. Every single warrior on Vaxi was punished for the crimes of Lord Romonav VII, either slain in battle or burned in massed pyres as tall as Warlord Titans.
In other words, business as usual for the Ordo Hereticus.
The Inquisitors saw what they had wrought, and deemed it sufficient: to carry on purging the heretics and fighting between themselves would only devastate the Sector further, and it was already almost defenseless against any outside threat. The traitorous governor was obviously purged in an appropriately public and gruesome manner, and all others saw the might of the Inquisition. Since then, all of the different Inquisitorial factions and heretic nobles act much more circumspectly, and try to avoid the repetition of such a cataclysmic event.
The loss of troops was great, but the loss of institutional knowledge in the Imperial Guard meant that the corpses of the defeated Orks were left unburned, which caused massive and regular outbreaks of feral Orks in centuries following the attrocity. Dark Eldar also started a string of mass kidnappings, which were stopped by the Imperial Navy on the world of Aventine, with the main guns of their ships. Surviving locals had a drop in appreciation of the Imperium and are tending towards separatism, with their planetary governor, Lord Sarawak also seeming to tend towards separatism and neglecting the psyker cull.
The Vaxi Atrocity was apparently planned by someone (or something). Of course the influential and powerful Inquisitor who confessed to this on his deathbed didn't name any individuals or factions before dying, but he did say that the Vaxi Atrocity wasn't just an attempt to do something: it was a success. What was achieved is unknown. A conclave of radical and successful Warp-savants known as the Abyssian Witnesses that studies the Pandaemonium warp storm noticed that its ebbs and flows were very odd during the Vaxi Atrocity (that's why they founded their order). Conveniently, there is/might be a group of Inquisitors known as The Storm Masters who seek to control the Pandaemonium, who seem to be the prime suspects. Obviously this might be a decoy (seeing as no Inquisitors have been formally identified as part of that group), and any number of radical groups could have masterminded the Atrocity (be they radicals like the or heretics).
The Vaxi Atrocity also spurred the rise of the so-called "Romonstrance" philosophy inside the ranks of the Inquisition. It holds that all Imperial institutions, including the Inquisition itself, are corrupt and should be torn down so that the entire structure by which humanity rules itself can be rebuilt. They believe that the original settlers in the Askellion Sector were fleeing some great injustice when they came to Askellon, unwilling to accept whatever regime held dominion at that shrouded time. All that has transpired in the galaxy, from the Age of Strife to the Great Crusade, through the Horus Heresy and into the Age of Imperium, these Inquisitors believe is the inevitable result of the evil of the regime those original colonists were fleeing. The Remonstrance wishes not just to tear down the Imperium, but to return it to an earlier, purer form, a template they believe is hidden in the very blood of the Lords of Askellon, passed down to them over countless generations. Seeing as the High Lords of Askellon are hinted to have sided with Horus during the Horus Heresy (and the population rose up against the Imperium under the leadership of a so-called "saint" during the Scouring) and are still traitorous, heretical and incompetent nowadays, this is unlikely to end well. To these people, the fact that the Pandaemonium appears inextricably linked to these noble houses and waxes and wanes in accordance to the fortunes of several of these High families is just a coincidence.